LEE- Yer Sistem Bilimi Lisansüstü Programı
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Yazar "Çoraman, Emrah" ile LEE- Yer Sistem Bilimi Lisansüstü Programı'a göz atma
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ÖgeAssessing the Bosphorus as a migratory corridor for Pipistrellus nathusii using acoustic monitoring methods(Graduate School, 2024-07-02) İlbaş, Tuğçe Nur ; Çoraman, Emrah ; 601211009 ; Earth System ScienceTürkiye has one of the richest bat diversity in the Mediterranean region. However, essential ecological information about bat species, such as population sizes, distributions and their migration behaviour is lacking. This information gap is primarily due to the elusive behavior of bats. Most of the bat research in Türkiye is about cave-dwelling species, which are relatively easier to study. Studies on other species, on the other hand, are generally based on opportunistic and non-systematic surveys. In this context, acoustic ecology methods offer an effective approach to investigating bats. This study aims to conduct a systematic acoustic ecology investigation in İstanbul, Türkiye, with a specific focus on the role of Bosphorus as a migratory corridor for bats. In particular, the migration patterns of Pipistrellus nathusii, a long-distance migratory bat species, were investigated. Additionally, the relationship between bat activity and meteorological parameters, as well as moon phases were explored to assess their impact on migration. Ultrasonic sound recordings were collected from four different locations along the Bosphorus, spanning from north to south, between April and November 2022. Recordings were preliminary analysed with Kaleidoscope Pro software and then processed manually. Analysis revealed that bat activity was positively related to temperature. Wind speed and direction affect bat activity in different ways depending on the season. In particular, light winds are positively associated with bat activity. When the effect of moon phases on bat activity was examined, it was found that the P. nathusii activity level in Yıldız City Park and ITU Campus was more affected by the moon phases, and especially the Nathusius Pipistrelle acoustic group activity decreased during the full moon phase. Pipistrellus nathusii activity in Yıldız City Park increased from mid-August and decreased towards the end of October. Activity on the ITU Campus started to increase in mid-August, peaked towards the end of September, and decreased at the end of October. Activity in the Atatürk City Forest started to increase in mid-August, peaked in September, and continued to decrease slightly in the autumn. In the Sarıyer Forest, there was an increase in August, the highest activity was seen in September and decreased with the end of the autumn. These findings show that the Bosphorus is a migratory corridor for P. nathusii. The insights gained from this study will contribute to the conservation of migratory bat routes between Europe and Asia.
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ÖgeEcological niche modeling of Myotis davidii(Graduate School, 2022-06-09) Aksakal, Emre Can ; Çoraman, Emrah ; 601181012 ; Earth System ScienceMyotis davidii is a whiskered bat species distributed in large areas of the Western Palaearctic. It has a cryptic sister species, Myotis mystacinus, which also has a similar distribution range in Europe and western Asia. The distribution of M. davidii extends from the Balkans to the Far East Asia, whereas M. mystacinus is found in Europe, Anatolia, and the Caucasus. They have a sympatric range in an area extending from the Balkans to the Transcaucasia via Anatolia. In this sympatric area, the populations of M. davidii had discordant patterns of mitochondrial and nuclear DNA, indicating that there were gene exchange between these species in the past. In this study, it was aimed to investigate the effects of the past climatic conditions on the evolutionary history of M. davidii and its cryptic sister species, M. mystacinus. The particular aims of this thesis are: 1) to construct the bioclimatic niches of M. davidii and M. mystacinus; 2) to identify their putative refugial areas during the last glacial period; and 3) to assess their responses to current climate change. In order to investigate these aims, ecological niche models were utilized. Ecological niche models aims to predict the distribution range of species by matching the environmental factors with species occurence points. Ecological niche modeling approach has become a common and practical application in conservation and biogeography study, especially with the advent of computer sciences and essential databases. In this study, ecological niche models are constructed by using the R programming language, as implemented in the BIOMOD2 package. A maximum entrophy appoach was used, which is a machine learning method developed for ecological niche modelling applications. The constructed models captured the current range of M. davidii but failed for M. mystacinus. For Myotis mystacinus, the lack of data from the Balkans and Anatolia was the likely reason for the unsuccessful model projections. The models for M. davidii suggest that inaccordance with the genetic lineages there might be to separate ecological units. Past projections suggest that Anatolia and the Balkans might have acted as refugial areas for both of the species during the Last Glacial Maximum. For M. davidii, the coastal regions of the Black Sea and the Mediterranean regions of Anatolia were likely refugial areas. These findings highlights the importance of Anatolia as a glacial refugium. Finally, the future projections suggested that there will major range shifts in the distribution of these species, especially for M. mystacinus moving towards norther Europe.
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ÖgeInvestigating the genomic differentiation landscape of the large mouse-eared bats(Graduate School, 2024-05-23) Şensoy, Bengisu ; Çoraman, Emrah ; 601211001 ; Earth System ScienceInterspecific gene flow, through shaping the evolution of species over time, plays a pivotal role in evolutionary biology. Often complex and multifaceted, this process presents a rich area to explore the intricate dynamics that drive the evolution of species. The large mouse-eared bats, specifically Myotis myotis and M. blythii, present a particularly intriguing species complex for studying interspecific gene flow. Myotis myotis and M. blythii have substantially overlapping ranges across Europe and Anatolia. These species also exhibit evidence of gene flow, identified in the previous studies. Their shared mitochondrial lineage suggests past hybridization events. Additionally, nuclear marker based analyses identified evidence of recent gene flow events. Despite their sympatric distribution coupled with past and present hybridization events, the mechanism underlying the maintenance of separate gene pools remains an intriguing question. This study aims to contribute in the understanding of the evolutionary history of the large Myotis bats through a whole-genome approach. In this regard, genomic differentiation landscapes were considered within and between Large Myotis bats. For the genomic analysis, whole-genome shotgun sequencing data was generated from a total of thirty-four samples, representing M. myotis, M. blythii, and their closely related species, M. punicus. To assess the population structures and differentiation levels, Principal Component and Admixture analyses were conducted. Both analyses identified three distinct clusters in accordance with the three large Myotis taxa. Within M. blythii, a further split separating the individuals from Kyrgyzstan and Mongolia from the rest was present. Genomic landscapes of differentiation were explored through Manhattan plots of fixation index, nucleotide diversity and genomic divergence. The genomic differentiation assessments supported the nuclear divergence of M. myotis and M. blythii. Within M. blythii, East and West populations exhibited a significant divergence, although not to a level comparable to the divergence seen between two different species. Potentially introgressed genomic regions were investigated. Although a slightly increased gene flow signal was observed across the entire genome between M. myotis and Eastern M. blythii, localized introgression regions that would indicate recent hybridization could not be detected. Further exploration of introgressed genomic regions may reveal the genomic basis for species differentiation. This study contributes to future studies on large Myotis bats and other cryptic species complexes, while also demonstrating the power of whole-genome data in unraveling the complex processes that shape the evolution of species.
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ÖgePhylogeography of the Savi's pipistrelle (Vespertilionidae, chiroptera) complex based on whole mitochondrial genome analysis(Graduate School, 2024-07-01) Ergöl, Yeliz ; Çoraman, Emrah ; 601211010 ; Earth System ScienceUnderstanding the phylogeography of species provides insight into the historical processes that lead the formation of their current geographic distributions and also how they evolve and adapt to variable environments over time. Intraspecific and interspecific genetic variations stand as a great indicator for elucidation of the evolutionary history of organisms in diverged phylogeographical patterns. Bats represent an immensely diverged group among mammals. They inhabit a wide variety of ecosystems, with the tropical belt hosting the highest number of bat species, similar to many other life forms. While the oldest known fossil of Chiroptera is approximately 52 million years old, they are hypothesized to be evolved around the Cretaceous-Tertiary boundary. During their evolution, they settled to the nocturnal niche. Echolocation and flight capabilities have affected the phylogenetic classification in the era of morphological and physiological taxonomy. However, the taxonomic classification of Chiroptera is a more complex phenomenon. The developments of modern genetic techniques transformed the historical perception of taxonomy. The introduction of high-throughput sequencing, which enables the sequencing of an organism's whole genetic material, has made genomic studies increasingly popular in biodiversity research. This powerful technique has revealed that organisms can exhibit significant genetic variation, even when their phenotypic characteristics do not reflect this diversity. Cryptic species, which arise from the discordance between morphological similarity and genetic divergence, exemplify this phenomenon. Resolving cryptic diversity is cruicial for identying evolutionary significant units and provides a new dimension for investigating the ecological dynamics of species. Furthermore, it is a significant concept in biodiversity assessment and monitoring, essential for inforimg conservation actions. Past studies have showned that the Palearctic Region hosts a rich fauna with signifacnt cryptic diversity, including among bats. Savi's Pipistrelle, Hypsugo savii, is a small-sized, vespertilionid bat species with a broad distribution range across various ecoregions in Europe, Asia, and North Africa. The accumulation of studies showing intraspecific variation within the species has drawn attention to the investigation of possible divergence within the taxon. Several studies idenfied deeply diverged mitochondrial lineages of H. savii. Two of such lineages have been proposed as distinct species statuses, H. darwinii and H. stubbei, based on their significant divergence from H.savii. Hypsugo savii hosts possibly further cryptic diversity. It is composed of deeply diverged clades, with sympatric occurences in Northwestern Africa, the Iberian Peninsula, Italy, and some Mediterranean islands (Sardinia, Sicily, and Malta). These studies, however, are based on limited sampling from a very broad geographical range. Furthermore, they utilize realtively short mitochondrial markers and marker selection is not usually consistent among studies. This study aims to invesitage the whole mitogemones of the previously identified H. savii lineages and the recently suggested related species. There are three main objectives: 1) establishing a reproducible workflow to de novo assemble mitogenome from whole genome sequencing data; 2) de novo assembling complete mitogenome of H. savii and the related species; and 3) reconstructing their phylogenetic relationships based on whole mitogenome sequences. Thirty samples from various regions including Central Asia, Sinai Peninsula, North Africa, continental Europea, and Mediterranean islands were analysed. High-throughput shotgun sequencing data was used for the analysis. The analysis workflow covers data filtering, de novo assembling of complete mitogenomes, and annotating the obtained mitogenomes. Complete mitochondrial genomes were succesfully de novo assembled for thirty samples, representing all of the previously identified lineages, as well as the closely related species, H. stubbei and H. alaschanicus. Mitochondrial genes were annotated on the assembled genomes. The read pool of each sample was mapped to the assembled mitogenomes to assess their coverage and also to edit possible misallignments and gaps. The samples which had uncircular genomes were manual edited and circularized. The tRNA profiles were analyzed with tRNAscan-SE. Phylogenetic relations of the analysed samples were investigated reconstructing phylogenetic trees. The sequences were aligned and the pairwise distance of the sequences were calculated with MEGA11. The phylogenies were obtained with Maximum-Likelihood model with IQ-TREE and RAxML tools. The trees were visualized with FigTree abd iTOL WebServer. The alignments were analysed with PopArt for a haplotype network analysis. The highly variable non-coding D-loop regions were removed from the sequences for all these analysis . All thirty-seven mitochondrial genes were annotated: two of them were ribosomal RNAs; twenty-two were transfer RNAs; and thirteen were protein-coding genes. D-loop regions of mitogenomes were also annotated. The secondary stuctures of the tRNA profiles were calculated and illustrated. The tRNA for serine amino acid was lacking the D- arm in the secondary stucture, which had no significant impact on its functionality. Phylogenetic analysis revealed that there are three main H. savii lineages in the Western Palearctic region. The related species, H. ariel, H.alaschanicus, and H. stubbei, also formed three distinct clusters. The latter was identified in Kyrgyzstan, which is outside of its known range. The distribution of Hypsugo savii lineages were in three main regions: Eastern Mediterranean, Western Mediterranean, and North African-Southwestern Mediterranean. In Sardinia, the latter of these three lineages were found together. The pairwise genetic distance between the clades in Europe were between 8 and 10%, close to the difference observed between H. alaschanicus and the other species. Similar levels of divergences were also found between newly proposed species, H. stubbei, and the European clades. These observed high levels of mitogenomic differences suggest that the H. savii complex probably harbours further cryptic diversity.